2OSO | pdb_00002oso

Crystal structure of a vinyl-4-reductase family protein (mj_1460) from methanocaldococcus jannaschii dsm at 1.90 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2OSD	PDB entry 2OSD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	277	NANODROP, 15.0% Glycerol, 0.17M NaOAc, 25.5% PEG 4000, 0.1M TRIS-HCL pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.1	α = 90
b = 42.1	β = 90
c = 172.4	γ = 120

Symmetry
Space Group	P 31 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing)	2007-01-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91162	SSRL	BL11-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.89	28.736	96	0.066	16.15			14775			32.942

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.89	1.96	69.4		0.504	2.5		1949

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2OSD	1.9	28.736	14719	743	99.35	0.192	0.192	0.189	0.19	0.245	0.25	RANDOM	24.066

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
1.27	0.63		1.27		-1.9

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.677
r_dihedral_angle_3_deg	16.509
r_dihedral_angle_1_deg	6.228
r_scangle_it	2.251
r_mcangle_it	2.231
r_angle_refined_deg	1.615
r_mcbond_it	1.579
r_scbond_it	1.579
r_angle_other_deg	0.954
r_mcbond_other	0.342
r_symmetry_vdw_refined	0.226
r_nbd_refined	0.207
r_xyhbond_nbd_refined	0.196
r_nbtor_refined	0.185
r_symmetry_hbond_refined	0.177
r_nbd_other	0.169
r_symmetry_vdw_other	0.154
r_metal_ion_refined	0.097
r_chiral_restr	0.095
r_nbtor_other	0.09
r_bond_refined_d	0.018
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1263
Nucleic Acid Atoms
Solvent Atoms	81
Heterogen Atoms	18

Software

Software
Software Name	Purpose
MolProbity	model building
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
PHASER	phasing